Job ID = 4287377 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-12-10T03:02:33 fasterq-dump.2.9.6 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) 2019-12-10T03:02:33 fasterq-dump.2.9.6 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) 2019-12-10T03:02:33 fasterq-dump.2.9.6 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) spots read : 15,191,493 reads read : 30,382,986 reads written : 15,191,493 reads 0-length : 15,191,493 rm: cannot remove ‘[DSE]RR*’: No such file or directory fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:01 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:09:11 15191493 reads; of these: 15191493 (100.00%) were unpaired; of these: 8313869 (54.73%) aligned 0 times 4633967 (30.50%) aligned exactly 1 time 2243657 (14.77%) aligned >1 times 45.27% overall alignment rate Time searching: 00:09:14 Overall time: 00:09:14 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 953 sequences. [bam_rmdupse_core] 387155 / 6877624 = 0.0563 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Tue, 10 Dec 2019 12:16:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX4654062/SRX4654062.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX4654062/SRX4654062.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX4654062/SRX4654062.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX4654062/SRX4654062.bam'] # control file = None # effective genome size = 2.15e+09 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Tue, 10 Dec 2019 12:16:23: #1 read tag files... INFO @ Tue, 10 Dec 2019 12:16:23: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 12:16:31: 1000000 INFO @ Tue, 10 Dec 2019 12:16:39: 2000000 INFO @ Tue, 10 Dec 2019 12:16:46: 3000000 INFO @ Tue, 10 Dec 2019 12:16:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX4654062/SRX4654062.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX4654062/SRX4654062.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX4654062/SRX4654062.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX4654062/SRX4654062.bam'] # control file = None # effective genome size = 2.15e+09 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Tue, 10 Dec 2019 12:16:53: #1 read tag files... INFO @ Tue, 10 Dec 2019 12:16:53: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 12:16:54: 4000000 INFO @ Tue, 10 Dec 2019 12:17:01: 5000000 INFO @ Tue, 10 Dec 2019 12:17:04: 1000000 INFO @ Tue, 10 Dec 2019 12:17:09: 6000000 INFO @ Tue, 10 Dec 2019 12:17:13: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 12:17:13: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 12:17:13: #1 total tags in treatment: 6490469 INFO @ Tue, 10 Dec 2019 12:17:13: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 12:17:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 10 Dec 2019 12:17:13: #1 tags after filtering in treatment: 6490208 INFO @ Tue, 10 Dec 2019 12:17:13: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 12:17:13: #1 finished! INFO @ Tue, 10 Dec 2019 12:17:13: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 12:17:13: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 12:17:14: 2000000 INFO @ Tue, 10 Dec 2019 12:17:14: #2 number of paired peaks: 6107 INFO @ Tue, 10 Dec 2019 12:17:14: start model_add_line... INFO @ Tue, 10 Dec 2019 12:17:14: start X-correlation... INFO @ Tue, 10 Dec 2019 12:17:14: end of X-cor INFO @ Tue, 10 Dec 2019 12:17:14: #2 finished! INFO @ Tue, 10 Dec 2019 12:17:14: #2 predicted fragment length is 51 bps INFO @ Tue, 10 Dec 2019 12:17:14: #2 alternative fragment length(s) may be 51,153,221,377,569 bps INFO @ Tue, 10 Dec 2019 12:17:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX4654062/SRX4654062.05_model.r WARNING @ Tue, 10 Dec 2019 12:17:14: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 10 Dec 2019 12:17:14: #2 You may need to consider one of the other alternative d(s): 51,153,221,377,569 WARNING @ Tue, 10 Dec 2019 12:17:14: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 10 Dec 2019 12:17:14: #3 Call peaks... INFO @ Tue, 10 Dec 2019 12:17:14: #3 Pre-compute pvalue-qvalue table... BedGraph に変換中... INFO @ Tue, 10 Dec 2019 12:17:23: 3000000 INFO @ Tue, 10 Dec 2019 12:17:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX4654062/SRX4654062.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX4654062/SRX4654062.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX4654062/SRX4654062.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX4654062/SRX4654062.bam'] # control file = None # effective genome size = 2.15e+09 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Tue, 10 Dec 2019 12:17:23: #1 read tag files... INFO @ Tue, 10 Dec 2019 12:17:23: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 12:17:32: 1000000 INFO @ Tue, 10 Dec 2019 12:17:32: 4000000 INFO @ Tue, 10 Dec 2019 12:17:35: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 12:17:40: 2000000 INFO @ Tue, 10 Dec 2019 12:17:41: 5000000 INFO @ Tue, 10 Dec 2019 12:17:45: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX4654062/SRX4654062.05_peaks.xls INFO @ Tue, 10 Dec 2019 12:17:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX4654062/SRX4654062.05_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 12:17:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX4654062/SRX4654062.05_summits.bed INFO @ Tue, 10 Dec 2019 12:17:45: Done! pass1 - making usageList (40 chroms): 2 millis pass2 - checking and writing primary data (753 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 12:17:48: 3000000 INFO @ Tue, 10 Dec 2019 12:17:50: 6000000 INFO @ Tue, 10 Dec 2019 12:17:55: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 12:17:55: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 12:17:55: #1 total tags in treatment: 6490469 INFO @ Tue, 10 Dec 2019 12:17:55: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 12:17:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 10 Dec 2019 12:17:55: #1 tags after filtering in treatment: 6490208 INFO @ Tue, 10 Dec 2019 12:17:55: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 12:17:55: #1 finished! INFO @ Tue, 10 Dec 2019 12:17:55: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 12:17:55: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 12:17:56: 4000000 INFO @ Tue, 10 Dec 2019 12:17:56: #2 number of paired peaks: 6107 INFO @ Tue, 10 Dec 2019 12:17:56: start model_add_line... INFO @ Tue, 10 Dec 2019 12:17:56: start X-correlation... INFO @ Tue, 10 Dec 2019 12:17:56: end of X-cor INFO @ Tue, 10 Dec 2019 12:17:56: #2 finished! INFO @ Tue, 10 Dec 2019 12:17:56: #2 predicted fragment length is 51 bps INFO @ Tue, 10 Dec 2019 12:17:56: #2 alternative fragment length(s) may be 51,153,221,377,569 bps INFO @ Tue, 10 Dec 2019 12:17:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX4654062/SRX4654062.10_model.r WARNING @ Tue, 10 Dec 2019 12:17:56: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 10 Dec 2019 12:17:56: #2 You may need to consider one of the other alternative d(s): 51,153,221,377,569 WARNING @ Tue, 10 Dec 2019 12:17:56: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 10 Dec 2019 12:17:56: #3 Call peaks... INFO @ Tue, 10 Dec 2019 12:17:56: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 12:18:04: 5000000 INFO @ Tue, 10 Dec 2019 12:18:11: 6000000 INFO @ Tue, 10 Dec 2019 12:18:15: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 12:18:15: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 12:18:15: #1 total tags in treatment: 6490469 INFO @ Tue, 10 Dec 2019 12:18:15: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 12:18:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 10 Dec 2019 12:18:16: #1 tags after filtering in treatment: 6490208 INFO @ Tue, 10 Dec 2019 12:18:16: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 12:18:16: #1 finished! INFO @ Tue, 10 Dec 2019 12:18:16: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 12:18:16: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 12:18:17: #2 number of paired peaks: 6107 INFO @ Tue, 10 Dec 2019 12:18:17: start model_add_line... INFO @ Tue, 10 Dec 2019 12:18:17: start X-correlation... INFO @ Tue, 10 Dec 2019 12:18:17: end of X-cor INFO @ Tue, 10 Dec 2019 12:18:17: #2 finished! INFO @ Tue, 10 Dec 2019 12:18:17: #2 predicted fragment length is 51 bps INFO @ Tue, 10 Dec 2019 12:18:17: #2 alternative fragment length(s) may be 51,153,221,377,569 bps INFO @ Tue, 10 Dec 2019 12:18:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX4654062/SRX4654062.20_model.r WARNING @ Tue, 10 Dec 2019 12:18:17: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 10 Dec 2019 12:18:17: #2 You may need to consider one of the other alternative d(s): 51,153,221,377,569 WARNING @ Tue, 10 Dec 2019 12:18:17: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 10 Dec 2019 12:18:17: #3 Call peaks... INFO @ Tue, 10 Dec 2019 12:18:17: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 12:18:17: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 12:18:27: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX4654062/SRX4654062.10_peaks.xls INFO @ Tue, 10 Dec 2019 12:18:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX4654062/SRX4654062.10_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 12:18:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX4654062/SRX4654062.10_summits.bed INFO @ Tue, 10 Dec 2019 12:18:27: Done! pass1 - making usageList (35 chroms): 1 millis pass2 - checking and writing primary data (436 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 12:18:38: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 12:18:48: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX4654062/SRX4654062.20_peaks.xls INFO @ Tue, 10 Dec 2019 12:18:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX4654062/SRX4654062.20_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 12:18:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX4654062/SRX4654062.20_summits.bed INFO @ Tue, 10 Dec 2019 12:18:48: Done! pass1 - making usageList (22 chroms): 2 millis pass2 - checking and writing primary data (155 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。